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SCARF2 scavenger receptor class F member 2 [ Homo sapiens (human) ]

Gene ID: 91179, updated on 11-Apr-2024

Summary

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Official Symbol
SCARF2provided by HGNC
Official Full Name
scavenger receptor class F member 2provided by HGNC
Primary source
HGNC:HGNC:19869
See related
Ensembl:ENSG00000244486 MIM:613619; AllianceGenome:HGNC:19869
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NSR1; SREC2; VDEGS; SREC-II; SRECRP-1
Summary
The protein encoded by this gene is similar to SCARF1/SREC-I, a scavenger receptor protein that mediates the binding and degradation of acetylated low density lipoprotein (Ac-LDL). This protein has only little activity of internalizing modified low density lipoproteins (LDL), but it can interact with SCARF1 through its extracellular domain. The association of this protein with SCARF1 is suppressed by the presence of scavenger ligands. Alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]
Expression
Broad expression in fat (RPKM 3.8), prostate (RPKM 3.4) and 24 other tissues See more
Orthologs
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Genomic context

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Location:
22q11.21
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (20424584..20437825, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (20828870..20842097, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (20778874..20792112, complement)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:20747551-20748540 Neighboring gene zinc finger protein 74 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_62654 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_62657 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:20764690-20764912 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_62670 Neighboring gene VISTA enhancer hs1620 Neighboring gene RNA, U6 small nuclear 225, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr22:20783264-20783430 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:20784487-20785326 Neighboring gene uncharacterized LOC107985588 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:20795983-20796484 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:20796485-20796984 Neighboring gene kelch like family member 22 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_62725 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_62734 Neighboring gene KLHL12 pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Two novel variants in SCARF2 gene underlie van den Ende-Gupta syndrome. Karaer D, et al. Am J Med Genet A, 2022 Jun. PMID 35224863
  2. Sclerocornea in a patient with van den Ende-Gupta syndrome homozygous for a SCARF2 microdeletion. Migliavacca MP, et al. Am J Med Genet A, 2014 May. PMID 24478002, Free PMC Article
  3. Mutations in SCARF2 are responsible for Van Den Ende-Gupta syndrome. Anastasio N, et al. Am J Hum Genet, 2010 Oct 8. PMID 20887961, Free PMC Article
  4. Further delineation of van den Ende-Gupta syndrome: Genetic heterogeneity and overlap with congenital heart defects and skeletal malformations syndrome. Hildebrandt CC, et al. Am J Med Genet A, 2021 Jul. PMID 33783941
  5. SREC-II, a new member of the scavenger receptor type F family, trans-interacts with SREC-I through its extracellular domain. Ishii J, et al. J Biol Chem, 2002 Oct 18. PMID 12154095

See all (18) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Two novel variants in SCARF2 gene underlie van den Ende-Gupta syndrome.
    Title: Two novel variants in SCARF2 gene underlie van den Ende-Gupta syndrome.
  2. Further delineation of van den Ende-Gupta syndrome: Genetic heterogeneity and overlap with congenital heart defects and skeletal malformations syndrome.
    Title: Further delineation of van den Ende-Gupta syndrome: Genetic heterogeneity and overlap with congenital heart defects and skeletal malformations syndrome.
  3. the full VDEGS phenotype may include sclerocornea resulting from homozygosity or compound heterozygosity for loss of function variants in SCARF2.
    Title: Sclerocornea in a patient with van den Ende-Gupta syndrome homozygous for a SCARF2 microdeletion.
  4. Mutations in SCARF2 are responsible for Van Den Ende-Gupta syndrome.
    Title: Mutations in SCARF2 are responsible for Van Den Ende-Gupta syndrome.
  5. SRECII binds to SRECI and has a similar tissue distribution pattern
    Title: SREC-II, a new member of the scavenger receptor type F family, trans-interacts with SREC-I through its extracellular domain.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Van den Ende-Gupta syndrome
MedGen: C1833136 OMIM: 600920 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables scavenger receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in vesicle-mediated transport IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in focal adhesion HDA PubMed 
located_in membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
scavenger receptor class F member 2
Names
scavenger receptor expressed by endothelial cells 2 protein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_031868.2 RefSeqGene

    Range
    5035..18276
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_153334.7 → NP_699165.3  scavenger receptor class F member 2 isoform 1 precursor

    See identical proteins and their annotated locations for NP_699165.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AF522196, BC009326
    Consensus CDS
    CCDS13779.2
    UniProtKB/Swiss-Prot
    E5RFB8, Q58A83, Q8IXF3, Q96GP6, Q9BW74
    Related
    ENSP00000485276.1, ENST00000623402.1
    Conserved Domains (1) summary
    PHA03247
    Location:534 → 871
    PHA03247; large tegument protein UL36; Provisional

  2. NM_182895.5 → NP_878315.2  scavenger receptor class F member 2 isoform 2 precursor

    See identical proteins and their annotated locations for NP_878315.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame segment within the coding region, as compared to variant 1. The resulting isoform (2) lacks an internal region, as compared to isoform 1.
    Source sequence(s)
    AB024433, BC009326
    Consensus CDS
    CCDS46666.1
    UniProtKB/Swiss-Prot
    Q96GP6
    Related
    ENSP00000477564.2, ENST00000622235.5
    Conserved Domains (1) summary
    PHA03247
    Location:529 → 866
    PHA03247; large tegument protein UL36; Provisional

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    20424584..20437825 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017029065.3 → XP_016884554.1  scavenger receptor class F member 2 isoform X2

  2. XM_047441585.1 → XP_047297541.1  scavenger receptor class F member 2 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    20828870..20842097 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054326108.1 → XP_054182083.1  scavenger receptor class F member 2 isoform X2

  2. XM_054326107.1 → XP_054182082.1  scavenger receptor class F member 2 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96GP6.5 GenPept UniProtKB/Swiss-Prot:Q96GP6

Gene LinkOut

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